working on current change

[mothur.git] / removegroupscommand.cpp

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 7034941e73e6a02ae07a02ab11631e8a7b752f3d..9b537281b4abef7ecb9f270e1438993fca198e22 100644 (file)
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -166,14 +166,17 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
                        accnosfile = validParameter.validFile(parameters, "accnos", true);
                        if (accnosfile == "not open") { abort = true; }
                        else if (accnosfile == "not found") {  accnosfile = ""; }       
+                       else { m->setAccnosFile(accnosfile); }
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
                        else if (fastafile == "not found") {  fastafile = "";  }        
+                       else { m->setFastaFile(fastafile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") {  namefile = "";  }  
+                       else { m->setNameFile(namefile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
@@ -182,15 +185,17 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
                                groupfile = m->getGroupFile(); 
                                if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setGroupFile(groupfile); }   
                        
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
+                       else { m->setListFile(listfile); }
                        
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxfile == "not open") { abort = true; }
                        else if (taxfile == "not found") {  taxfile = "";  }
+                       else { m->setTaxonomyFile(taxfile); }
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }